Journal ArticleDOI
Beta diversity as the variance of community data: dissimilarity coefficients and partitioning.
TLDR
The approach links the concept of beta diversity with the analysis of community data by commonly used methods like ordination and anova, and addressed the question of which index to use by coding 16 indices using 14 properties that are necessary for beta assessment, comparability among data sets, sampling issues and ordination.Abstract:
Beta diversity can be measured in different ways. Among these, the total variance of the community data table Y can be used as an estimate of beta diversity. We show how the total variance of Y can be calculated either directly or through a dissimilarity matrix obtained using any dissimilarity index deemed appropriate for pairwise comparisons of community composition data. We addressed the question of which index to use by coding 16 indices using 14 properties that are necessary for beta assessment, comparability among data sets, sampling issues and ordination. Our comparison analysis classified the coefficients under study into five types, three of which are appropriate for beta diversity assessment. Our approach links the concept of beta diversity with the analysis of community data by commonly used methods like ordination and anova. Total beta can be partitioned into Species Contributions (SCBD: degree of variation of individual species across the study area) and Local Contributions (LCBD: comparative indicators of the ecological uniqueness of the sites) to Beta Diversity. Moreover, total beta can be broken up into within- and among-group components by manova, into orthogonal axes by ordination, into spatial scales by eigenfunction analysis or among explanatory data sets by variation partitioning.read more
Citations
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Journal ArticleDOI
Interpreting the replacement and richness difference components of beta diversity
TL;DR: This paper first reviews the historical development of the formulae for decomposing dissimilarities into replacement, richness difference and nestedness indices, and shows that local contributions of replacement and richness difference to total beta diversity can be computed and mapped.
Journal ArticleDOI
Unifying Species Diversity, Phylogenetic Diversity, Functional Diversity, and Related Similarity and Differentiation Measures Through Hill Numbers
Anne Chao,Chun-Huo Chiu,Lou Jost +2 more
TL;DR: This work provides a unified method of decomposing these diversities and constructing normalized taxonomic, phylogenetic, and functional similarity and differentiation measures, including N-assemblage phylogenetic or functional generalizations of species diversity.
Journal ArticleDOI
Ecologists should not use statistical significance tests to interpret simulation model results
TL;DR: This article argues that modelers should abandon frequentist statistical hypothesis tests applied to simulation model output as a misuse of statistical theory, and encourages instead a focus on the magnitude of differences between simulations.
Unifying Species Diversity, Phylogenetic Diversity, Functional Diversity, and Related Similarity and Differentiation Measures
Anne Chao,Chun-Huo Chiu,Lou Jost +2 more
TL;DR: In this paper, the authors present a taxonomic, phylogenetic, and functional framework for attribute diversity, which unifies ecologists' measures of species diversity,phylogenetic diversity, and distance-based functional diversity.
Journal ArticleDOI
The initial state of the human gut microbiome determines its reshaping by antibiotics
Frédéric Raymond,Amin Ahmed Ouameur,Maxime Déraspe,Naeem Iqbal,Hélène Gingras,Bédis Dridi,Philippe Leprohon,Pier-Luc Plante,Richard Giroux,Ève Bérubé,Johanne Frenette,Dominique K. Boudreau,Jean-Luc Simard,Isabelle Chabot,Marc-Christian Domingo,Sylvie Trottier,Maurice Boissinot,Ann Huletsky,Paul H. Roy,Marc Ouellette,Michel G. Bergeron,Jacques Corbeil +21 more
TL;DR: It is shown that standard antibiotic treatment can alter the gut microbiome in a specific, reproducible and predictable manner, and a subgroup of participants who were enriched in the opportunistic pathogen Enterobacter cloacae after exposure to the antibiotic, an effect linked to lower initial microbiome diversity and to a Bacteroides enterotype is identified.
References
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An Ordination of the Upland Forest Communities of Southern Wisconsin
Roger H. Bray,John T. Curtis +1 more
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Marc Dufrêne,Pierre Legendre +1 more
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Journal ArticleDOI
Ecologically meaningful transformations for ordination of species data
TL;DR: Transitions are proposed for species data tables which allow ecologists to use ordination methods such as PCA and RDA for the analysis of community data, while circumventing the problems associated with the Euclidean distance, and avoiding CA and CCA which present problems of their own in some cases.